Mutagenetix > Incidental Mutation

Incidental Mutation 'R5802:Loxl3'

448780

Institutional Source

Beutler Lab

Gene Symbol

Loxl3

Ensembl Gene

ENSMUSG00000000693

Gene Name

lysyl oxidase-like 3

Synonyms

Lor2

MMRRC Submission

043391-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.922) question?

Stock #

R5802 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

83034173-83052562 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 83049289 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 453 (T453A)

Ref Sequence

ENSEMBL: ENSMUSP00000000707 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000000707] [ENSMUST00000089645] [ENSMUST00000101257] [ENSMUST00000113962] [ENSMUST00000113963] [ENSMUST00000122955] [ENSMUST00000134606]

AlphaFold

Q9Z175

Predicted Effect

possibly damaging
Transcript: ENSMUST00000000707
AA Change: T453A

PolyPhen 2 Score 0.665 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000000707
Gene: ENSMUSG00000000693
AA Change: T453A

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
SR	45	146	2.1e-50	SMART
SR	170	283	1.09e-25	SMART
SR	308	408	3.72e-51	SMART
SR	418	526	8.5e-37	SMART
Pfam:Lysyl_oxidase	530	730	3.9e-103	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000089645

SMART Domains

Protein: ENSMUSP00000087073
Gene: ENSMUSG00000068329

Domain	Start	End	E-Value	Type
low complexity region	28	39	N/A	INTRINSIC
transmembrane domain	106	125	N/A	INTRINSIC
low complexity region	128	143	N/A	INTRINSIC
Pfam:Trypsin	170	341	1.1e-14	PFAM
Pfam:Trypsin_2	182	320	1.2e-34	PFAM
PDZ	371	445	2.86e-10	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000101257

SMART Domains

Protein: ENSMUSP00000098815
Gene: ENSMUSG00000000693

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
SR	45	146	2.1e-50	SMART
SR	170	283	1.09e-25	SMART
SR	308	396	5.46e-17	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000113962

SMART Domains

Protein: ENSMUSP00000109595
Gene: ENSMUSG00000068329

Domain	Start	End	E-Value	Type
low complexity region	28	39	N/A	INTRINSIC
transmembrane domain	106	125	N/A	INTRINSIC
low complexity region	128	143	N/A	INTRINSIC
Pfam:Trypsin_2	182	237	2.7e-12	PFAM
Pfam:Trypsin	212	277	4.5e-6	PFAM
PDZ	285	348	4.89e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000113963

SMART Domains

Protein: ENSMUSP00000109596
Gene: ENSMUSG00000068329

Domain	Start	End	E-Value	Type
low complexity region	28	39	N/A	INTRINSIC
transmembrane domain	106	125	N/A	INTRINSIC
low complexity region	128	143	N/A	INTRINSIC
Pfam:Trypsin	170	342	6.8e-15	PFAM
Pfam:Trypsin_2	182	320	7.1e-24	PFAM
PDZ	350	413	4.89e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000122955

SMART Domains

Protein: ENSMUSP00000138153
Gene: ENSMUSG00000068329

Domain	Start	End	E-Value	Type
low complexity region	28	39	N/A	INTRINSIC
transmembrane domain	106	125	N/A	INTRINSIC
low complexity region	128	143	N/A	INTRINSIC
Pfam:Trypsin	170	321	2.1e-10	PFAM
Pfam:Trypsin_2	182	317	9.5e-21	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000132099

Predicted Effect

probably benign
Transcript: ENSMUST00000134606

SMART Domains

Protein: ENSMUSP00000115547
Gene: ENSMUSG00000068329

Domain	Start	End	E-Value	Type
Pfam:Trypsin	7	180	2.7e-15	PFAM
Pfam:Trypsin_2	20	158	3.1e-24	PFAM
PDZ	209	283	2.86e-10	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144058

Predicted Effect

probably benign
Transcript: ENSMUST00000150217

SMART Domains

Protein: ENSMUSP00000118234
Gene: ENSMUSG00000068329

Domain	Start	End	E-Value	Type
low complexity region	4	11	N/A	INTRINSIC
Pfam:Trypsin	41	215	1.6e-11	PFAM
Pfam:Trypsin_2	53	190	1.8e-31	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154829

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155502

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184661

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204318

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000203339

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000204281

Meta Mutation Damage Score

0.1081

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.7%

Validation Efficiency

97% (63/65)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a lysyl oxidase, which likely functions as an amine oxidase and plays a role in the formation of crosslinks in collagens and elastin. Deletion of the related gene in mouse causes neonatal mortality with cleft palate, spine deformity, and defects in collagen organization. A mutation in this gene was found in a family with Stickler syndrome. [provided by RefSeq, Sep 2016]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit lethality shortly after birth, craniofacial and vertebral abnormalities associated with collagen deformities. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A830018L16Rik	A	T	1: 11,950,964	D383V	probably damaging	Het
Abca4	A	T	3: 122,054,232	L67F	probably damaging	Het
Abcc9	C	A	6: 142,656,676		probably null	Het
Atp2a3	T	C	11: 72,972,882	V175A	probably damaging	Het
B3galt4	T	A	17: 33,950,757	D169V	probably damaging	Het
Bsn	C	T	9: 108,113,009	R1848Q	possibly damaging	Het
Camkk2	T	C	5: 122,734,244	E90G	probably damaging	Het
Cdon	T	A	9: 35,454,420	I155N	probably damaging	Het
Cep70	A	G	9: 99,296,405	N519D	probably damaging	Het
Clgn	T	C	8: 83,425,614	S582P	probably damaging	Het
Cnga3	T	C	1: 37,260,925	F280S	probably damaging	Het
Dennd4c	C	T	4: 86,811,453	T764M	probably benign	Het
Dis3	A	T	14: 99,099,664	S4T	probably damaging	Het
Dlgap1	T	C	17: 70,766,091		probably null	Het
Dnah17	C	T	11: 118,036,446	V3839I	possibly damaging	Het
Dnajc1	A	G	2: 18,284,739	Y286H	probably benign	Het
Dynap	T	A	18: 70,241,002	D151V	unknown	Het
Ednrb	A	G	14: 103,821,714	F292S	probably damaging	Het
Eef1a1	A	G	9: 78,479,036	S396P	probably damaging	Het
Fancg	A	G	4: 43,006,582	F324S	probably benign	Het
Fbxw11	T	A	11: 32,711,790	S56T	probably benign	Het
Gm13178	T	A	4: 144,703,636	D261V	probably damaging	Het
Gm14409	T	C	2: 177,265,256	T150A	possibly damaging	Het
Gm17535	G	C	9: 3,035,758	V209L	probably benign	Homo
Gm20767	G	A	13: 120,154,913	S96N	possibly damaging	Het
Gm5592	C	T	7: 41,219,105		probably benign	Het
Gm7030	A	G	17: 36,111,287		probably benign	Het
Gpr137	C	T	19: 6,942,005	W51*	probably null	Het
Hbb-bs	T	C	7: 103,826,672	Y146C	probably damaging	Het
Herc1	G	T	9: 66,462,878	C2982F	probably damaging	Het
Hnrnpa3	T	A	2: 75,665,056	N309K	unknown	Het
Hydin	A	T	8: 110,452,060	I1096F	possibly damaging	Het
Klf12	A	G	14: 100,022,894	V133A	probably benign	Het
Lats2	A	T	14: 57,694,418	Y848N	probably damaging	Het
Ltn1	T	G	16: 87,415,681	H664P	probably benign	Het
Lypd6	C	T	2: 50,173,601	T40I	probably benign	Het
Nbeal1	A	T	1: 60,272,221	T1817S	probably benign	Het
Nub1	A	C	5: 24,702,441	Y350S	possibly damaging	Het
Pbp2	A	G	6: 135,309,876	Y158H	possibly damaging	Het
Ptpru	C	T	4: 131,788,377	E827K	possibly damaging	Het
Rap1a	A	G	3: 105,745,936	Y32H	probably damaging	Het
Raph1	T	C	1: 60,488,673	N1143S	possibly damaging	Het
Rbl1	T	C	2: 157,161,433	T859A	probably benign	Het
Rom1	A	G	19: 8,928,824	L117P	probably damaging	Het
Senp6	T	C	9: 80,118,644		probably benign	Het
Sirpb1c	T	C	3: 15,832,076	M379V	probably benign	Het
Slc6a4	C	T	11: 77,019,236	T439M	probably damaging	Het
Srsf12	G	T	4: 33,230,929	R141L	probably damaging	Het
Stk10	C	T	11: 32,596,748	P335L	probably benign	Het
Tecpr1	A	T	5: 144,206,546	N670K	probably benign	Het
Tgds	T	C	14: 118,132,707	E8G	probably benign	Het
Tmem129	A	G	5: 33,657,716	S38P	probably damaging	Het
Trappc9	T	C	15: 72,685,339	E812G	probably damaging	Het
Trmt10b	T	A	4: 45,314,236		probably benign	Het
Wapl	A	G	14: 34,692,320	T380A	probably damaging	Het
Xylt1	A	T	7: 117,656,691	T829S	probably benign	Het
Zc3h6	C	T	2: 129,015,559	P666L	possibly damaging	Het
Zfp703	C	T	8: 26,979,205	P299L	probably damaging	Het

Other mutations in Loxl3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00957:Loxl3	APN	6	83048766	unclassified	probably benign
IGL01370:Loxl3	APN	6	83049487	missense	probably damaging	1.00
IGL02126:Loxl3	APN	6	83048647	missense	probably damaging	1.00
IGL02128:Loxl3	APN	6	83050583	missense	probably damaging	1.00
R0241:Loxl3	UTSW	6	83050133	missense	probably damaging	1.00
R0241:Loxl3	UTSW	6	83050133	missense	probably damaging	1.00
R1725:Loxl3	UTSW	6	83035593	missense	probably benign	0.00
R1771:Loxl3	UTSW	6	83049909	missense	probably damaging	1.00
R2017:Loxl3	UTSW	6	83048977	missense	probably damaging	0.99
R2291:Loxl3	UTSW	6	83037488	missense	probably benign	0.07
R3731:Loxl3	UTSW	6	83050671	critical splice donor site	probably null
R4179:Loxl3	UTSW	6	83037584	missense	probably benign	0.00
R5230:Loxl3	UTSW	6	83035794	missense	probably benign	0.16
R5385:Loxl3	UTSW	6	83050612	missense	probably damaging	0.99
R5591:Loxl3	UTSW	6	83048037	missense	probably damaging	1.00
R5664:Loxl3	UTSW	6	83049882	missense	probably benign	0.12
R5769:Loxl3	UTSW	6	83050600	missense	probably damaging	0.98
R5771:Loxl3	UTSW	6	83035799	splice site	probably null
R5831:Loxl3	UTSW	6	83049018	missense	probably benign	0.01
R5945:Loxl3	UTSW	6	83037511	missense	probably damaging	1.00
R6542:Loxl3	UTSW	6	83048166	missense	probably benign	0.00
R6687:Loxl3	UTSW	6	83050664	missense	probably damaging	1.00
R7961:Loxl3	UTSW	6	83050809	missense	possibly damaging	0.88
R8009:Loxl3	UTSW	6	83050809	missense	possibly damaging	0.88
R8122:Loxl3	UTSW	6	83049259	missense	probably damaging	1.00
R8278:Loxl3	UTSW	6	83048716	missense	probably damaging	1.00
R8373:Loxl3	UTSW	6	83048891	missense	possibly damaging	0.89
R8411:Loxl3	UTSW	6	83050624	missense	probably damaging	1.00
R8539:Loxl3	UTSW	6	83049526	missense	probably benign
R8684:Loxl3	UTSW	6	83035585	missense	probably benign	0.23
R8782:Loxl3	UTSW	6	83048070	missense	probably benign
R8801:Loxl3	UTSW	6	83048648	missense	probably damaging	1.00
R8859:Loxl3	UTSW	6	83037545	missense	probably damaging	1.00
R8864:Loxl3	UTSW	6	83035758	missense	probably damaging	0.99
R9031:Loxl3	UTSW	6	83035522	missense	probably damaging	1.00
R9081:Loxl3	UTSW	6	83048657	missense	possibly damaging	0.67
R9176:Loxl3	UTSW	6	83049311	missense	probably damaging	0.99
R9369:Loxl3	UTSW	6	83050412	missense	probably benign	0.26
R9634:Loxl3	UTSW	6	83050854	missense	probably benign	0.10
V1024:Loxl3	UTSW	6	83035738	missense	probably damaging	1.00
X0009:Loxl3	UTSW	6	83038480	missense	probably damaging	1.00
Z1177:Loxl3	UTSW	6	83038578	nonsense	probably null
Z1177:Loxl3	UTSW	6	83048160	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TTTCTACTCAGGCCCGGACATC -3'
(R):5'- TCCAGTGAGGTTATAGGTTCCAG -3'

Sequencing Primer
(F):5'- ACAGCCCTGCCATCTGTGAG -3'
(R):5'- ATAGGTTCCAGTTTCCAGGGCC -3'

Posted On

2016-12-15